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My guess is those hyphens are being rendered on the fly by the reader. Calibre's not the culprit here. You didn't mention what you were viewing the newly made mobi with, but I assume it's either the Kindle Previewer (emulating Kindle for iPhone) or the actual Kindle for iPhone App—which hyphenates.
Would need to see the source of the epub in question to verify, but I don't think it's calibre's fault since the mobi format Amazon (and calibre) uses doesn't have any inherent hyphenization ability. That's more than likely a feature of the rendering app.
Change the font-size you're viewing the mobi with and see if the hyphen isn't relocated.
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